Have you a dual core CPU?
I ask because some of ATi's cards (the Radeon HD 4xx0 series, namely) offloads alot of it's work onto the CPU, starving PCSX2 of that CPU power, so in the end, it's like downgrading your CPU, because PCSX2 gets less since the ATi card is using some. PCSX2 is CPU limited, not GPU limited, in most cases.
Also, another thing worth mentioning is that it's been said that this "issue" was fixed in newer drivers, but I haven't seen anything of that claim. I was always aware it was how it worked, and not an "issue" per se, but I don't know. If you have the newest drivers and a dual core CPU, either the "problem" still exists with ATi cards, or it's just your system in some other way.
What was the previous nVidia GPU, by the way.